1
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Soni R, Carmichael JP, Shah ZH, Murray JA. A family of cyclin D homologs from plants differentially controlled by growth regulators and containing the conserved retinoblastoma protein interaction motif. THE PLANT CELL 1995; 7:85-103. [PMID: 7696881 PMCID: PMC160767 DOI: 10.1105/tpc.7.1.85] [Citation(s) in RCA: 203] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A new family of three related cyclins has been identified in Arabidopsis by complementation of a yeast strain deficient in G1 cyclins. Individual members show tissue-specific expression and are conserved in other plant species. They form a distinctive group of plant cyclins, which we named delta-type cyclins to indicate their similarities with mammalian D-type cyclins. The sequence relationships between delta and D cyclins include the N-terminal sequence LXCXE. This motif was originally identified in certain viral oncoproteins and is strongly implicated in binding to the retinoblastoma protein pRb. By analogy to mammalian cyclin D, these plant homologs may mediate growth and phytohormonal signals into the plant cell cycle. In support of this hypothesis, we show that, on restimulation of suspension-cultured cells, cyclin delta 3 is rapidly induced by the plant growth regulator cytokinin and cyclin delta 2 is induced by carbon source.
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30 |
203 |
2
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Abstract
The formation of capsular contracture around silicone implants continues to be the most common complication of augmentation mammaplasty. To date, the etiologic factors in the formation of capsular contractures have remained inconclusive. In the present study, the role of subclinical infection with S. epidermidis as a cause of capsular contracture was evaluated in 16 rabbits using miniature silicone implants. All the implants on the side contaminated with varying concentrations of S. epidermidis developed breast capsular contractures. Using Baker's classification, they were graded III or IV, while the controls were all considered to be either grade I or II. Grossly, the capsules on the contaminated side were firm, fibrous, and 2 to 3 times thicker than the controls, and this was confirmed histologically using micrometry. Implants contaminated with 10(7) bacteria uniformly extruded. The present study seems to indicate that subclinical infection with Staphylococcus epidermidis may be one of the causes of capsular contracture around breast implants.
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44 |
102 |
3
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Dandachli W, Kannan V, Richards R, Shah Z, Hall-Craggs M, Witt J. Analysis of cover of the femoral head in normal and dysplastic hips: new CT-based technique. ACTA ACUST UNITED AC 2008; 90:1428-34. [PMID: 18978260 DOI: 10.1302/0301-620x.90b11.20073] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present a new CT-based method which measures cover of the femoral head in both normal and dysplastic hips and allows assessment of acetabular inclination and anteversion. A clear topographical image of the head with its covered area is generated. We studied 36 normal and 39 dysplastic hips. In the normal hips the mean cover was 73% (66% to 81%), whereas in the dysplastic group it was 51% (38% to 64%). The significant advantage of this technique is that it allows the measurements to be standardised with reference to a specific anatomical plane. When this is applied to assessing cover in surgery for dysplasia of the hip it gives a clearer understanding of where the corrected hip stands in relation to normal and allows accurate assessment of inclination and anteversion.
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Journal Article |
17 |
93 |
4
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Toivonen JM, O'Dell KM, Petit N, Irvine SC, Knight GK, Lehtonen M, Longmuir M, Luoto K, Touraille S, Wang Z, Alziari S, Shah ZH, Jacobs HT. Technical knockout, a Drosophila model of mitochondrial deafness. Genetics 2001; 159:241-54. [PMID: 11560901 PMCID: PMC1461776 DOI: 10.1093/genetics/159.1.241] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mutations in mtDNA-encoded components of the mitochondrial translational apparatus are associated with diverse pathological states in humans, notably sensorineural deafness. To develop animal models of such disorders, we have manipulated the nuclear gene for mitochondrial ribosomal protein S12 in Drosophila (technical knockout, tko). The prototypic mutant tko(25t) exhibits developmental delay, bang sensitivity, impaired male courtship, and defective response to sound. On the basis of a transgenic reversion test, these phenotypes are attributable to a single substitution (L85H) at a conserved residue of the tko protein. The mutant is hypersensitive to doxycyclin, an antibiotic that selectively inhibits mitochondrial protein synthesis, and mutant larvae have greatly diminished activities of mitochondrial redox enzymes and decreased levels of mitochondrial small-subunit rRNA. A second mutation in the tko gene, Q116K, which is predicted to impair the accuracy of mitochondrial translation, results in the completely different phenotype of recessive female sterility, based on three independent transgenic insertions. We infer that the tko(25t) mutant provides a model of mitochondrial hearing impairment resulting from a quantitative deficiency of mitochondrial translational capacity.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Anti-Bacterial Agents/pharmacology
- Blotting, Northern
- Blotting, Southern
- Cell Nucleus/genetics
- Cloning, Molecular
- Crosses, Genetic
- DNA, Mitochondrial/genetics
- Deafness/genetics
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Doxycycline/pharmacology
- Drosophila/genetics
- Drosophila/physiology
- Female
- Humans
- Infertility, Female/genetics
- Male
- Mitochondria/metabolism
- Models, Genetic
- Mutation
- Oligonucleotides/metabolism
- Oxidation-Reduction
- Phenotype
- Polymerase Chain Reaction
- Protein Biosynthesis
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/physiology
- Sequence Analysis, DNA
- Sound
- Time Factors
- Transgenes
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24 |
76 |
5
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Kalueff AV, Minasyan A, Keisala T, Shah ZH, Tuohimaa P. Hair barbering in mice: implications for neurobehavioural research. Behav Processes 2005; 71:8-15. [PMID: 16236465 DOI: 10.1016/j.beproc.2005.09.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Revised: 07/14/2005] [Accepted: 09/11/2005] [Indexed: 01/03/2023]
Abstract
Barbering (fur/whisker trimming, the Dalila effect) is a behaviour-associated hair and whisker loss frequently seen in laboratory rodents, including mice. Here we analyse barbering behaviour in 129S1, NMRI, C57BL/6 and BALB/c mouse strains and some of their F1 hybrids. Our study shows that barbering in mice, depending on their genotype, is a complex behaviour with several distinct contexts or domains. We observed social (dominant) barbering in NMRI and C57BL/6 mice, sexual over-grooming in 129S1 and C57BL/6 mice, maternal barbering in lactating 129S1 and C57BL/6 mice, and stress-evoked barbering in F1 (NMRIx129S1) hybrids. In contrast, aggressive BALB/c mice and their F1 progeny do not use barbering in their behaviour. We suggest that barbering may be an important complex multi-domain behaviour sensitive to various manipulations, and represent a useful index in neurobehavioural research.
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Research Support, Non-U.S. Gov't |
20 |
76 |
6
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:1875. [PMID: 29382843 PMCID: PMC5789830 DOI: 10.1038/s41598-018-19535-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022] Open
Abstract
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
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Research Support, Non-U.S. Gov't |
7 |
73 |
7
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Shah ZH, Rehman HM, Akhtar T, Alsamadany H, Hamooh BT, Mujtaba T, Daur I, Al Zahrani Y, Alzahrani HAS, Ali S, Yang SH, Chung G. Humic Substances: Determining Potential Molecular Regulatory Processes in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:263. [PMID: 29593751 PMCID: PMC5861677 DOI: 10.3389/fpls.2018.00263] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/14/2018] [Indexed: 05/20/2023]
Abstract
Humic substances (HSs) have considerable effects on soil fertility and crop productivity owing to their unique physiochemical and biochemical properties, and play a vital role in establishing biotic and abiotic interactions within the plant rhizosphere. A comprehensive understanding of the mode of action and tissue distribution of HS is, however, required, as this knowledge could be useful for devising advanced rhizospheric management practices. These substances trigger various molecular processes in plant cells, and can strengthen the plant's tolerance to various kinds of abiotic stresses. HS manifest their effects in cells through genetic, post-transcriptional, and post-translational modifications of signaling entities that trigger different molecular, biochemical, and physiological processes. Understanding of such fundamental mechanisms will provide a better perspective for defining the cues and signaling crosstalk of HS that mediate various metabolic and hormonal networks operating in plant systems. Various regulatory activities and distribution strategies of HS have been discussed in this review.
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Review |
7 |
52 |
8
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Stijf-Bultsma Y, Sommer L, Tauber M, Baalbaki M, Giardoglou P, Jones DR, Gelato KA, van Pelt J, Shah Z, Rahnamoun H, Toma C, Anderson KE, Hawkins P, Lauberth SM, Haramis APG, Hart D, Fischle W, Divecha N. The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output. Mol Cell 2015; 58:453-67. [PMID: 25866244 PMCID: PMC4429956 DOI: 10.1016/j.molcel.2015.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 01/20/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022]
Abstract
Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein-associated factor with important roles in transcription regulation, pluripotency, and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.
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10 |
45 |
9
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Shah ZH, Hakkaart GA, Arku B, de Jong L, van der Spek H, Grivell LA, Jacobs HT. The human homologue of the yeast mitochondrial AAA metalloprotease Yme1p complements a yeast yme1 disruptant. FEBS Lett 2000; 478:267-70. [PMID: 10930580 DOI: 10.1016/s0014-5793(00)01859-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In yeast, three AAA superfamily metalloproteases (Yme1p, Afg3p and Rca1p) are localized to the mitochondrial inner membrane where they perform roles in the assembly and turnover of the respiratory chain complexes. We have investigated the function of the proposed human orthologue of yeast Yme1p, encoded by the YME1L gene on chromosome 10p. Transfection of both HEK-293EBNA and yeast cells with a green fluorescent protein-tagged YME1L cDNA confirmed mitochondrial targeting. When expressed in a yme1 disruptant yeast strain, YME1L restored growth on glycerol at 37 degrees C. We propose that YME1L plays a phylogenetically conserved role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies.
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25 |
35 |
10
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Abstract
We have characterized nuclear genes for mitoribosomal protein S12 (mt-rps12) a major component of the ribosomal accuracy centre, in human, mouse and Drosophila melanogaster. In human and Drosophila, and probably also in mouse, there is a single intron within the coding region, located in the mitochondrial targeting pre-sequence. In humans, the mRNA structure is highly suggestive of translational regulation. In all three species, there is an amino-acid substitution with respect to eubacterial homologues in a residue implicated in aminoglycoside resistance. The only viable mutant allele of the Drosophila gene, associated with a bang-sensitive phenotype (paralysis upon mechanical vibration, arising from a mechanoreceptor cell defect) also has a novel substitution in a conserved region implicated in translational fidelity. Given the involvement of the mitoribosomal accuracy centre in human sensorineural deafness by virtue of rRNA mutations, our results indicate that this fly mutant may be a useful animal model of this disorder, and earmark the gene for mt-rps12 as a candidate in human hearing impairment.
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28 |
32 |
11
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Mamoon Rehman H, Amjad Nawaz M, Bao L, Hussain Shah Z, Lee JM, Ahmad MQ, Chung G, Yang SH. Genome-wide analysis of Family-1 UDP-glycosyltransferases in soybean confirms their abundance and varied expression during seed development. JOURNAL OF PLANT PHYSIOLOGY 2016; 206:87-97. [PMID: 27721120 DOI: 10.1016/j.jplph.2016.08.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 08/23/2016] [Accepted: 08/28/2016] [Indexed: 05/13/2023]
Abstract
Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences. Phylogenetic analysis against 22 referenced UGTs from Arabidopsis and maize clustered the putative UGTs into 15 major groups (A-O); J, K, and N were not represented, but the UGTs were distributed across all chromosomes except chromosome 04. Leucine was the most abundant amino acid across all 149 UGT peptide sequences. Two conserved introns (C1 and C2) were detected in the most intron-containing UGTs. Publicly available microarray data on their maximum expression in the seed developmental stage were further confirmed using Affymetrix soybean IVT array and RNA sequencing data. The UGT expression models were designed, based on reads per kilobase of gene model per million mapped read (RPKM) values confirmed their maximally varied expression at globular and early maturation stages of seed development.
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9 |
32 |
12
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Rehman HM, Nawaz MA, Shah ZH, Daur I, Khatoon S, Yang SH, Chung G. In-Depth Genomic and Transcriptomic Analysis of Five K + Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation. FRONTIERS IN PLANT SCIENCE 2017; 8:804. [PMID: 28588592 PMCID: PMC5440519 DOI: 10.3389/fpls.2017.00804] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/28/2017] [Indexed: 05/27/2023]
Abstract
Plants have evolved a sophisticated network of K+ transport systems to regulate growth and development. Limited K+ resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K+ transporters in plants. Here, we have identified 70 putative K+ transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K+ channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K+ inventories in all other plants.
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research-article |
8 |
26 |
13
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Juhola MK, Shah ZH, Grivell LA, Jacobs HT. The mitochondrial inner membrane AAA metalloprotease family in metazoans. FEBS Lett 2000; 481:91-5. [PMID: 10996302 DOI: 10.1016/s0014-5793(00)01989-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three metalloproteases belonging to the AAA superfamily (Yme1p, Afg3p and Rca1p) are involved in protein turnover and respiratory chain complex assembly in the yeast inner mitochondrial membrane. Analysis of the completed genome sequences of Caenorhabditis elegans and Drosophila melanogaster indicates that this gene family typically comprises 3-4 members in metazoans. Phylogenetic analysis reveals three main branches represented, respectively, by Saccharomyces cerevisiae YME1, human SPG7 (paraplegin) and S. cerevisiae AFG3 and RCA1. mt-AAA metalloproteases are weak candidates for several previously studied Drosophila mutants. A full elucidation of the cellular and physiological roles of mt-AAA metalloproteases in metazoans will require the creation of targeted mutations.
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Review |
25 |
25 |
14
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Shah Z, Lehman JA, Stevenson G. Capsular contracture around silicone implants: the role of intraluminal antibiotics. Plast Reconstr Surg 1982; 69:809-14. [PMID: 7071226 DOI: 10.1097/00006534-198205000-00016] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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43 |
23 |
15
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Abstract
Increasing innovation in rapid prototyping (RP) and additive manufacturing (AM), also known as 3D printing, is bringing about major changes in translational surgical research. This review describes the current position in the use of additive manufacturing in orthopaedic surgery. Cite this article: Bone Joint J 2018;100-B:455-60.
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Review |
7 |
22 |
16
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Shah ZH, Rehman HM, Akhtar T, Daur I, Nawaz MA, Ahmad MQ, Rana IA, Atif RM, Yang SH, Chung G. Redox and Ionic Homeostasis Regulations against Oxidative, Salinity and Drought Stress in Wheat (A Systems Biology Approach). Front Genet 2017; 8:141. [PMID: 29089961 PMCID: PMC5651134 DOI: 10.3389/fgene.2017.00141] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/21/2017] [Indexed: 01/21/2023] Open
Abstract
Systems biology and omics has provided a comprehensive understanding about the dynamics of the genome, metabolome, transcriptome, and proteome under stress. In wheat, abiotic stresses trigger specific networks of pathways involved in redox and ionic homeostasis as well as osmotic balance. These networks are considerably more complicated than those in model plants, and therefore, counter models are proposed by unifying the approaches of omics and stress systems biology. Furthermore, crosstalk among these pathways is monitored by the regulation and streaming of transcripts and genes. In this review, we discuss systems biology and omics as a promising tool to study responses to oxidative, salinity, and drought stress in wheat.
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Review |
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21 |
17
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Mariottini P, Shah ZH, Toivonen JM, Bagni C, Spelbrink JN, Amaldi F, Jacobs HT. Expression of the gene for mitoribosomal protein S12 is controlled in human cells at the levels of transcription, RNA splicing, and translation. J Biol Chem 1999; 274:31853-62. [PMID: 10542210 DOI: 10.1074/jbc.274.45.31853] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human gene RPMS12 encodes a protein similar to bacterial ribosomal protein S12 and is proposed to represent the human mitochondrial orthologue. RPMS12 reporter gene expression in cultured human cells supports the idea that the gene product is mitochondrial and is localized to the inner membrane. Human cells contain at least four structurally distinct RPMS12 mRNAs that differ in their 5'-untranslated region (5'-UTR) as a result of alternate splicing and of 5' end heterogeneity. All of them encode the same polypeptide. The full 5'-UTR contains two types of sequence element implicated elsewhere in translational regulation as follows: a short upstream open reading frame and an oligopyrimidine tract similar to that found at the 5' end of mRNAs encoding other growth-regulated proteins, including those of cytosolic ribosomes. The fully spliced (short) mRNA is the predominant form in all cell types studied and is translationally down-regulated in cultured cells in response to serum starvation, even though it lacks both of the putative translational regulatory elements. By contrast, other splice variants containing one or both of these elements are not translationally regulated by growth status but are translated poorly in both growing and non-growing cells. Reporter analysis identified a 26-nucleotide tract of the 5'-UTR of the short mRNA that is essential for translational down-regulation in growth-inhibited cells. Such experiments also confirmed that the 5'-UTR of the longer mRNA variants contains negative regulatory elements for translation. Tissue representation of RPMS12 mRNA is highly variable, following a typical mitochondrial pattern, but the relative levels of the different splice variants are similar in different tissues. These findings indicate a complex, multilevel regulation of RPMS12 gene expression in response to signals mediating growth, tissue specialization, and probably metabolic needs.
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18
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Daur I, Saad MM, Eida AA, Ahmad S, Shah ZH, Ihsan MZ, Muhammad Y, Sohrab SS, Hirt H. Boosting Alfalfa ( Medicago sativa L.) Production With Rhizobacteria From Various Plants in Saudi Arabia. Front Microbiol 2018; 9:477. [PMID: 29670582 PMCID: PMC5893776 DOI: 10.3389/fmicb.2018.00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022] Open
Abstract
This study focused on rhizobacteria to promote sustainable crop production in arid regions of Saudi Arabia. The study isolated 17 tightly root-adhering rhizobacteria from various plants at Hada Al Sham in Saudi Arabia. All 17 rhizobacterial isolates were confirmed as plant growth promoting rhizobacteria by classical biochemical tests. Using 16S rDNA gene sequence analyses, the strains were identified as Bacillus, Acinetobacter and Enterobacter. Subsequently, the strains were assessed for their ability to improve the physiology, nutrient uptake, growth, and yield of alfalfa plants grown under desert agriculture conditions. The field trials were conducted in a randomized complete block design. Inoculation of alfalfa with any of these 17 strains improved the relative water content; chlorophyll a; chlorophyll b; carotenoid contents; nitrogen (N), phosphorus, and potassium contents; plant height; leaf-to-stem ratio; and fresh and dry weight. Acinetobacter pittii JD-14 was most effective to increase fresh and dry weight of alfalfa by 41 and 34%, respectively, when compared to non-inoculated control plants. Nevertheless, all strains enhanced crop traits when compared to controls plants, indicating that these desert rhizobacterial strains could be used to develop an eco-friendly biofertilizer for alfalfa and possibly other crop plants to enhance sustainable production in arid regions.
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Journal Article |
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19
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Shah ZH, Migliosi V, Miller SC, Wang A, Friedman TB, Jacobs HT. Chromosomal locations of three human nuclear genes (RPSM12, TUFM, and AFG3L1) specifying putative components of the mitochondrial gene expression apparatus. Genomics 1998; 48:384-8. [PMID: 9545647 DOI: 10.1006/geno.1997.5166] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have mapped the chromosomal locations of three human nuclear genes for putative components of the apparatus of mitochondrial gene expression, using a combination of in situ hybridization and interspecies hybrid mapping. The genes RPMS12 (mitoribosomal protein S12, a conserved protein component of the mitoribosomal accuracy center), TUFM (mitochondrial elongation factor EF-Tu), and AFG3L1 (similar to the yeast genes Afg3 and Rca1 involved in the turnover of mistranslated or misfolded mtDNA-encoded polypeptides) were initially characterized by a combination of database sequence analysis, PCR, cloning, and DNA sequencing. RPMS12 maps to chromosome 19q13.1, close to the previously mapped gene for autosomal dominant hearing loss DFNA4. The TUFM gene is located on chromosome 16p11.2, with a putative pseudogene or variant (TUFML) located very close to the centromere of chromosome 17. AFG3L1 is located on chromosome 16q24, very close to the telomere. By virtue of their inferred functions in mitochondria, these genes should be regarded as candidates of disorders sharing features with mitochondrial disease syndromes, such as sensorineural deafness, diabetes, and retinopathy.
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20
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Abrahams S, Cavet G, Oakenfull EA, Carmichael JP, Shah ZH, Soni R, Murray JA. A novel and highly divergent Arabidopsis cyclin isolated by complementation in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1539:1-6. [PMID: 11389963 DOI: 10.1016/s0167-4889(01)00106-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel cyclin, CycJ18, was isolated by complementation of G1 cyclin-deficient budding yeast with an Arabidopsis cDNA library. CycJ18 shares only 20% identity in its conserved cyclin box domain with other cyclins, and is predominantly expressed in young seedlings. CycJ18 is a member of a potential new plant cyclin class.
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Alsamadany H, Alzahrani Y, Shah ZH. Physiomorphic and molecular-based evaluation of wheat germplasm under drought and heat stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1107945. [PMID: 37123840 PMCID: PMC10131247 DOI: 10.3389/fpls.2023.1107945] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Drought and heat stress are potential problems that can reduce wheat yield, particularly during the terminal growth stages in arid and semiarid regions of the world. The current study intended to examine the impact of individual and combined drought and heat stress on the biochemical contents (antioxidant enzymes, proline, soluble proteins, and soluble sugars), physiological parameters (chlorophyll content, cell membrane stability, photosynthesis, stomatal conductance, and transpiration), plant-water relations (relative water content, water potential, osmotic potential, and pressure potential), agronomic traits (flag leaf area, plant height, number of tillers per plant, spike length, grains per spike, and thousand-grain weight), and gene expression (TaHSF1a, TaWRKY-33, TaNAC2L, and TaGASR1) in four different thermostable and drought-tolerant wheat genotypes (i.e., Gold-16, HS-240, Suntop, and Hemai-13) collected from different countries. The tri-replicate experiment was conducted using two factorial arrangements in a randomized complete block design (RCBD). All measured traits, except total soluble sugars, proline, and cell membrane stability index, showed significant reduction under both combined and individual treatments. Furthermore, correlation analysis revealed a significant association between biochemical and physiological characteristics and crop agronomic productivity. Furthermore, principal component analysis (PCA) and heatmap analysis demonstrated significant levels of variation in traits according to the type of stress and nature of wheat genotype. The spectrographs and micrographs generated by scanning electron microscopy for the selected high- and low- tolerance samples revealed clear differences in mineral distribution and starch granulation. All studied genes showed comparatively high levels of relative expression under combined treatments of drought and heat stress in all wheat genotypes, but this expression was the highest in 'Gold-16' followed by 'HS-240', 'Suntop', and 'Hemai-13'. Overall, this study concluded that plants are proactive entities and they respond to stresses at all levels; however, the tolerant plants tend to retain the integrity of their biochemical, physiological, and molecular equilibrium.
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Shah ZH, Toompuu M, Hakkinen T, Rovio AT, van Ravenswaay C, De Leenheer EM, Smith RJ, Cremers FP, Cremers CW, Jacobs HT. Novel coding-region polymorphisms in mitochondrial seryl-tRNA synthetase (SARSM) and mitoribosomal protein S12 (RPMS12) genes in DFNA4 autosomal dominant deafness families. Hum Mutat 2001; 17:433-4. [PMID: 11317363 DOI: 10.1002/humu.1123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two genes for components of the mitochondrial translational apparatus, mitochondrial seryl-tRNA synthetase (SARSM) and mitoribosomal protein S12 (RPMS12) lie adjacent to one another on human chromosome 19, within the critical interval for the autosomal dominant deafness locus DFNA4. Both genes are plausible candidates for DFNA4, based on the fact that deafness mutations in mtDNA have been mapped both to tRNA-ser(UCN) and to the accuracy domain of the small subunit rRNA. We have sequenced the coding regions, proximal promoters, 5' and 3' UTR and splice junctional regions of both genes in two families with DFNA4-linked deafness and in controls. Novel polymorphisms 84425C>T, 83907A>G, 79485T>G, 79406C>T, 71755A>C and 68686C>G (numbered as in GenBank AC011455) were found in one or both families, but none is a plausible disease-causing mutation. Although regulatory mutations affecting either gene could still be involved in the phenotype, structural gene mutations affecting SARSM or RPMS12 can be excluded from consideration as the cause of DFNA4-linked deafness, at least in the families identified thus far.
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MESH Headings
- Chromosomes, Human, Pair 19/genetics
- DNA Mutational Analysis
- DNA Primers/genetics
- DNA, Intergenic/genetics
- Exons/genetics
- Family
- Genes, Dominant/genetics
- HeLa Cells
- Hearing Loss, Sensorineural/congenital
- Hearing Loss, Sensorineural/genetics
- Humans
- Mitochondria/chemistry
- Mitochondria/enzymology
- Netherlands
- Polymorphism, Genetic/genetics
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- RNA Splice Sites/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Ribosomal Proteins/genetics
- Serine-tRNA Ligase/genetics
- United States
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Ahmed Z, Shah ZH, Rehman HM, Shahzad K, Daur I, Elfeel A, Hassan MU, Elsafori AK, Yang SH, Chung G. Genomics: A Hallmark to Monitor Molecular and Biochemical Processes Leading Toward a Better Perceptive of Seed Aging and ex-situ Conservation. Curr Issues Mol Biol 2016; 22:89-112. [PMID: 27801354 DOI: 10.21775/cimb.022.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
For human food security, the preservation of 7.4 million ex-situ germplasm is a global priority. However, ex-situ-conserved seeds are subject to aging, which reduces their viability and ultimately results in the loss of valuable genetic material over long periods. Recent progress in seed biology and genomics has revealed new opportunities to improve the long-term storage of ex-situ seed germplasm. This review summarizes the recent improvements in seed physiology and genomics, with the intention of developing genomic tools for evaluating seed aging. Several lines of seed biology research have shown promise in retrieving viability signal from various stages of seed germination. We conclude that seed aging is associated with mitochondrial alteration and programmed cell death, DNA and enzyme repair, anti-oxidative genes, telomere length, and epigenetic regulation. Clearly, opportunities exist for observing seed aging for developing genomic tools to increment the traditional germination test for effective conservation of ex-situ germplasm.
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Tariq M, Sharif M, Shah Z, Khan R. Effect of foliar application of micronutrients on the yield and quality of sweet orange (Citrus Sinensis L.). Pak J Biol Sci 2007; 10:1823-8. [PMID: 19086544 DOI: 10.3923/pjbs.2007.1823.1828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
An experiment was designed to study the effect of foliar application of micronutrients on the yield, quality and leaf composition of sweet orange, Blood red variety at Shabazgari, Mardan. The experiment was laid out in a randomized complete block design in 2) factorial arrangement. Zinc, manganese and boron were applied as foliar spray at the rate of 0.4, 0.2 and 0.04 kg ha(-1), respectively in the presence of 1.56 kg N ha(-1) as urea and 0.4 kg surfactance ha(-1) (as wetting agent) in 400 L of water. The maximum fruit yield was obtained, when 0.4 kg Zn ha(-1) and 0.2 kg Mn ha(-1) was sprayed along with 1.56 kg N ha(-1) and 0.4 kg surfactance ha(-1) in 400 L of water. The minimum % peel was obtained with B alone and minimum % rag with Zn + Mn, maximum fruit size with Zn + B and maximum fruit volume with Zn + Mn. Similarly, % juice in sweet oranges was increased significantly by B alone, reducing sugar by Mn alone and vitamin C contents by Zn + B through foliar spray, suggested that each micronutrient had different role on the quality of citrus fruit. Foliar spray of Zn, Mn and B along with urea significantly increased the concentration of Zn and Mn in citrus leaves, while the concentration of B was not affected with foliar spray, perhaps due to dilution within the citrus tissues. Therefore, it is suggested that either Zn+Mn or Zn+B may be applied as foliar spray in combination with urea and surfactance for getting the maximum yield and improved quality of citrus fruit under prevailing conditions.
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