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Ping L, Zhengyang Z, Mohan S, Ruihong W, Zhengang L, Wen L, Xuemeng J, Yue C, Xinjun D, Shuo W. Effects and molecular mechanism of sugar transporter ESA_RS15745 on desiccation resistance, motility, and biofilm formation of Cronobacter sakazakii. J Food Sci 2024; 89:581-595. [PMID: 38126106 DOI: 10.1111/1750-3841.16872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/05/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Cronobacter sakazakii, an important Gram-negative foodborne pathogen, can cause neonatal meningitis and sepsis with high rates of infection and death. Gene ESA_RS15745 encodes a sugar transporter protein, which is not only essential for osmotic pressure maintenance during bacterial growth and reproduction but also associated with their desiccation tolerance, motility, and biofilm formation. Here, a mutant strain of ESA_RS15745 (ΔESA_RS15745) and the complementation strain (cpESA_RS15745) were constructed using a suicide vector knockout and gene complementation. ΔESA_RS15745 was found to have a decrease in its ability to transport maltose and trehalose and resist desiccation, whereas an increase in the ability of motility and biofilm formation, implying that ESA_RS15745 may positively regulate sugar transport and desiccation tolerance and negatively regulate motility and biofilm formation. To further investigate the molecular mechanisms underlying the function of related genes, RNA-seq was performed to explore the differentially expressed genes in the mutants. RNA-seq results showed the upregulation of 114 genes (mainly including those regulating chemotaxis and flagellar motility) and the downregulation of 22 genes (mainly including those regulating sugar transport). qRT-PCR analysis supported the RNA-seq results and showed that ESA_RS15745 may influence the dehydration tolerance though decreasing the intracellular trehalose content and negatively regulate the motility though the chemotactic signaling pathway. In addition, the biofilm formation of C. sakazakii should also be speculated to negatively regulate by ESA_RS15745 by consuming the extracellular carbohydrates concentration and then downregulating the intracellular cyclic diguanosine monophosphate. This study offers a reference for comprehending the molecular mechanism of gene ESA_RS15745 in C. sakazakii.
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Affiliation(s)
- Li Ping
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Zhang Zhengyang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Si Mohan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Wang Ruihong
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Li Zhengang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Lv Wen
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Ji Xuemeng
- Tianjin Key Laboratory of Food Science and Health, College of Medicine, Nankai University, Tianjin, China
| | - Cheng Yue
- School of Science, Tianjin University, Tianjin, China
| | - Du Xinjun
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Wang Shuo
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Food Science and Health, College of Medicine, Nankai University, Tianjin, China
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Straub K, Linde M, Kropp C, Blanquart S, Babinger P, Merkl R. Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. Biol Chem 2019; 400:367-381. [PMID: 30763032 DOI: 10.1515/hsz-2018-0344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/07/2018] [Indexed: 11/15/2022]
Abstract
For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.
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Affiliation(s)
- Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Mona Linde
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Cosimo Kropp
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Samuel Blanquart
- University of Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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Daniel J, Abraham L, Martin A, Pablo X, Reyes S. Rv2477c is an antibiotic-sensitive manganese-dependent ABC-F ATPase in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2018; 495:35-40. [DOI: 10.1016/j.bbrc.2017.10.168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
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4
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Gerke M, Bornberg-Bauer E, Jiang X, Fuellen G. Finding Common Protein Interaction Patterns Across Organisms. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein interactions are an important resource to obtain an understanding of cell function. Recently, researchers have compared networks of interactions in order to understand network evolution. While current methods first infer homologs and then compare topologies, we here present a method which first searches for interesting topologies and then looks for homologs. PINA (protein interaction network analysis) takes the protein interaction networks of two organisms, scans both networks for subnetworks deemed interesting, and then tries to find orthologs among the interesting subnetworks. The application is very fast because orthology investigations are restricted to subnetworks like hubs and clusters that fulfill certain criteria regarding neighborhood and connectivity. Finally, the hubs or clusters found to be related can be visualized and analyzed according to protein annotation.
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Affiliation(s)
- Mirco Gerke
- Division of Bioinformatics, Biology Department, Schlossplatz 4, D-48149 Münster, Germany
- Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, D- 48149 Münster, Germany
| | - Erich Bornberg-Bauer
- Division of Bioinformatics, Biology Department, Schlossplatz 4, D-48149 Münster, Germany
| | - Xiaoyi Jiang
- Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, D- 48149 Münster, Germany
| | - Georg Fuellen
- Division of Bioinformatics, Biology Department, Schlossplatz 4, D-48149 Münster, Germany
- Department of Medicine, AG Bioinformatics, Domagkstr. 3, D-48149 Münster, Germany
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Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily. Sci Rep 2015; 5:16724. [PMID: 26577702 PMCID: PMC4649718 DOI: 10.1038/srep16724] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/19/2015] [Indexed: 01/12/2023] Open
Abstract
The ATP binding cassette (ABC) transporters superfamily is one of the largest classes of membrane proteins. The core of the ABC transporter protein is composed of transmembrane domains (TMDs) and nucleotide binding domains (NBD). Eukaryotes ABC transporters are classified into seven main families (ABCA to ABCG) based on sequence similarity and domain organizations. With different domain number and domain organizations, eukaryote ABC transporters show diverse structures: the single structure (NBD or TMD), the ABC2 structure (NBD-NBD), the half structure (TMD-NBD or NBD-TMD) and the full structure (TMD-NBD-TMD-NBD or NBD-TMD-NBD-TMD). However, studies on how various ABC transporter gene structures evolved is still absent. Therefore, in this study, we comprehensively investigated the structural evolution of eukaryotic ABC transporters. The seven eukaryote ABC transporter families (A to G) fell into three groups: A&G group, B,C&D group and E&F group. There were at least four times the number of NBD and TMD fusion events in the origin of the half structure transporter. Two fusion modes were found in the full and ABC2 structure origination. Based on these findings, we present a putative structural evolutionary path of eukaryote ABC transporters that will increase our understanding on their origin, divergence and function.
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Evidence for an alternative genomic structure, mRNA and protein sequence of human ABCA13. Gene 2013; 515:298-307. [DOI: 10.1016/j.gene.2012.11.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/21/2012] [Accepted: 11/29/2012] [Indexed: 11/21/2022]
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Lewis VG, Ween MP, McDevitt CA. The role of ATP-binding cassette transporters in bacterial pathogenicity. PROTOPLASMA 2012; 249:919-942. [PMID: 22246051 DOI: 10.1007/s00709-011-0360-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 11/29/2011] [Indexed: 05/31/2023]
Abstract
The ATP-binding cassette transporter superfamily is present in all three domains of life. This ubiquitous class of integral membrane proteins have diverse biological functions, but their fundamental role involves the unidirectional translocation of compounds across cellular membranes in an ATP coupled process. The importance of this class of proteins in eukaryotic systems is well established as typified by their association with genetic diseases and roles in the multi-drug resistance of cancer. In stark contrast, the ABC transporters of prokaryotes have not been exhaustively investigated due to the sheer number of different roles and organisms in which they function. In this review, we examine the breadth of functions associated with microbial ABC transporters in the context of their contribution to bacterial pathogenicity and virulence.
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Affiliation(s)
- Victoria G Lewis
- Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, 5005, Australia
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Claisse O, Lonvaud-Funel A. Development of a multilocus variable number of tandem repeat typing method for Oenococcus oeni. Food Microbiol 2012; 30:340-7. [DOI: 10.1016/j.fm.2012.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/03/2012] [Accepted: 01/03/2012] [Indexed: 11/24/2022]
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Abstract
In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.
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Offer SM, Pan-Hammarström Q, Hammarström L, Harris RS. Unique DNA repair gene variations and potential associations with the primary antibody deficiency syndromes IgAD and CVID. PLoS One 2010; 5:e12260. [PMID: 20805886 PMCID: PMC2923613 DOI: 10.1371/journal.pone.0012260] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/17/2010] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Despite considerable effort, the genetic factors responsible for >90% of the antibody deficiency syndromes IgAD and CVID remain elusive. To produce a functionally diverse antibody repertoire B lymphocytes undergo class switch recombination. This process is initiated by AID-catalyzed deamination of cytidine to uridine in switch region DNA. Subsequently, these residues are recognized by the uracil excision enzyme UNG2 or the mismatch repair proteins MutSalpha (MSH2/MSH6) and MutLalpha (PMS2/MLH1). Further processing by ubiquitous DNA repair factors is thought to introduce DNA breaks, ultimately leading to class switch recombination and expression of a different antibody isotype. METHODOLOGY/PRINCIPAL FINDINGS Defects in AID and UNG2 have been shown to result in the primary immunodeficiency hyper-IgM syndrome, leading us to hypothesize that additional, potentially more subtle, DNA repair gene variations may underlie the clinically related antibody deficiencies syndromes IgAD and CVID. In a survey of twenty-seven candidate DNA metabolism genes, markers in MSH2, RAD50, and RAD52 were associated with IgAD/CVID, prompting further investigation into these pathways. Resequencing identified four rare, non-synonymous alleles associated with IgAD/CVID, two in MLH1, one in RAD50, and one in NBS1. One IgAD patient carried heterozygous non-synonymous mutations in MLH1, MSH2, and NBS1. Functional studies revealed that one of the identified mutations, a premature RAD50 stop codon (Q372X), confers increased sensitivity to ionizing radiation. CONCLUSIONS Our results are consistent with a class switch recombination model in which AID-catalyzed uridines are processed by multiple DNA repair pathways. Genetic defects in these DNA repair pathways may contribute to IgAD and CVID.
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Affiliation(s)
- Steven M. Offer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
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11
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Kos V, Ford RC. The ATP-binding cassette family: a structural perspective. Cell Mol Life Sci 2009; 66:3111-26. [PMID: 19544044 PMCID: PMC11115812 DOI: 10.1007/s00018-009-0064-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 05/27/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
Abstract
The ATP-binding cassette family is one of the largest groupings of membrane proteins, moving allocrites across lipid membranes, using energy from ATP. In bacteria, they reside in the inner membrane and are involved in both uptake and export. In eukaryotes, these transporters reside in the cell's internal membranes as well as in the plasma membrane and are unidirectional-out of the cytoplasm. The range of substances that these proteins can transport is huge, which makes them interesting for structure-function studies. Moreover, their abundance in nature has made them targets for structural proteomics consortia. There are eight independent structures for ATP-binding cassette transporters, making this one of the best characterised membrane protein families. Our understanding of the mechanism of transport across membranes and membrane protein structure in general has been enhanced by recent developments for this family.
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Affiliation(s)
- Veronica Kos
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Robert Curtis Ford
- Faculty of Life Sciences, Manchester Interdisplinary Biocentre, The University of Manchester, Manchester, M1 7DN UK
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12
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ATP-binding cassette transporters in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1757-71. [DOI: 10.1016/j.bbamem.2008.06.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 06/10/2008] [Accepted: 06/12/2008] [Indexed: 12/14/2022]
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13
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Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008; 72:317-64, table of contents. [PMID: 18535149 DOI: 10.1128/mmbr.00031-07] [Citation(s) in RCA: 933] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.
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Fuellen G. Homology and phylogeny and their automated inference. Naturwissenschaften 2008; 95:469-81. [PMID: 18288471 DOI: 10.1007/s00114-008-0348-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 12/20/2007] [Accepted: 01/12/2008] [Indexed: 11/25/2022]
Abstract
The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this "historical" approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of 'my closest relative looks and behaves like I do', often referred to as 'guilt by association'. To enable knowledge transfer on a large scale, several automated 'phylogenomics pipelines' have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.
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Affiliation(s)
- Georg Fuellen
- Bioinformatics Research Group, Institute for Mathematics and Computer Science, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany.
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Stolle K, Schnoor M, Fuellen G, Spitzer M, Cullen P, Lorkowski S. Cloning, genomic organization, and tissue-specific expression of the RASL11B gene. ACTA ACUST UNITED AC 2007; 1769:514-24. [PMID: 17628721 DOI: 10.1016/j.bbaexp.2007.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/25/2007] [Accepted: 05/29/2007] [Indexed: 01/22/2023]
Abstract
RASL11B is a member of the small GTPase protein family with a high degree of similarity to RAS proteins. Cloning of RASL11B mRNA and in silico analyses revealed that the human RASL11B gene spans about 4.5 kb and comprises four exons on chromosomal locus 4q12. The proximal 5'-flanking region of the gene lacks a TATA box but is GC-rich and contains a CCAAT box and several Sp1 sites. Consistent with this, the RASL11B gene was found to be expressed in all tissues investigated, with highest levels in placenta and in primary macrophages. The predicted RASL11B protein has no typical prenylation signal, indicating that it is probably not anchored to cellular membranes. RASL11B was induced during maturation of THP-1 monocytic cells into macrophage-like cells and in coronary artery smooth muscle cells after treatment with TGF-beta1. These results indicate that RASL11B may play a role in TGF-beta1-mediated developmental processes and in pathophysiologies such as inflammation, cancer, and arteriosclerosis.
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Affiliation(s)
- Katrin Stolle
- Leibniz Institute of Arteriosclerosis Research, University of Münster, Germany
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Lin T, Islam O, Heese K. ABC transporters, neural stem cells and neurogenesis – a different perspective. Cell Res 2006; 16:857-71. [PMID: 17088897 DOI: 10.1038/sj.cr.7310107] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Stem cells intrigue. They have the ability to divide exponentially, recreate the stem cell compartment, as well as create differentiated cells to generate tissues. Therefore, they should be natural candidates to provide a renewable source of cells for transplantation applied in regenerative medicine. Stem cells have the capacity to generate specific tissues or even whole organs like the blood, heart, or bones. A subgroup of stem cells, the neural stem cells (NSCs), is characterized as a self-renewing population that generates neurons and glia of the developing brain. They can be isolated, genetically manipulated and differentiated in vitro and reintroduced into a developing, adult or a pathologically altered central nervous system. NSCs have been considered for use in cell replacement therapies in various neurodegenerative diseases such as Parkinson's disease and Alzheimer's disease. Characterization of genes with tightly controlled expression patterns during differentiation represents an approach to understanding the regulation of stem cell commitment. The regulation of stem cell biology by the ATP-binding cassette (ABC) transporters has emerged as an important new field of investigation. As a major focus of stem cell research is in the manipulation of cells to enable differentiation into a targeted cell population; in this review, we discuss recent literatures on ABC transporters and stem cells, and propose an integrated view on the role of the ABC transporters, especially ABCA2, ABCA3, ABCB1 and ABCG2, in NSCs' proliferation, differentiation and regulation, along with comparisons to that in hematopoietic and other stem cells.
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Affiliation(s)
- Tingting Lin
- Department of Molecular and Cell Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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Lott PL, Mundry M, Sassenberg C, Lorkowski S, Fuellen G. Simplifying gene trees for easier comprehension. BMC Bioinformatics 2006; 7:231. [PMID: 16643669 PMCID: PMC1473203 DOI: 10.1186/1471-2105-7-231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 04/27/2006] [Indexed: 12/01/2022] Open
Abstract
Background In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important. Results We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree. Conclusion Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at .
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Affiliation(s)
- Paul-Ludwig Lott
- Division of Bioinformatics, Biology Department, University Münster, Schlossplatz 4, 48149 Münster, Germany
- Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, 48149 Münster, Germany
| | - Marvin Mundry
- Division of Bioinformatics, Biology Department, University Münster, Schlossplatz 4, 48149 Münster, Germany
- Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, 48149 Münster, Germany
- Department of Medicine, AG Bioinformatics, University Münster, Domagkstrasse 3, 48149 Münster, Germany
| | - Christoph Sassenberg
- Division of Bioinformatics, Biology Department, University Münster, Schlossplatz 4, 48149 Münster, Germany
- Institut für Informatik, Fachbereich Mathematik und Informatik, Einsteinstr. 62, 48149 Münster, Germany
| | - Stefan Lorkowski
- Leibniz-Institute of Arteriosclerosis Research, University Münster, Domagkstrasse 3, 48149 Münster, Germany
- Institute of Biochemistry, University Münster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Georg Fuellen
- Division of Bioinformatics, Biology Department, University Münster, Schlossplatz 4, 48149 Münster, Germany
- Department of Medicine, AG Bioinformatics, University Münster, Domagkstrasse 3, 48149 Münster, Germany
- Institute of Mathematics and Computer Science, University Greifswald, Jahnstrasse 15a, 17489 Greifswald, Germany
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18
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Spitzer M, Lorkowski S, Cullen P, Sczyrba A, Fuellen G. IsoSVM--distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics 2006; 7:110. [PMID: 16519805 PMCID: PMC1431569 DOI: 10.1186/1471-2105-7-110] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 03/06/2006] [Indexed: 11/24/2022] Open
Abstract
Background Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not. Results The IsoSVM tool introduces an automated approach to identifying isoforms on the protein level using a support vector machine (SVM) classifier. Based on three specific features used as input of the SVM classifier, it is possible to automatically identify isoforms with little effort and with an accuracy of more than 97%. We show that the SVM is superior to a radial basis function network and to a linear classifier. As an example application we use IsoSVM to estimate that a set of Xenopus laevis EST clusters consists of approximately 81% cases where sequences are each other's paralogs and 19% cases where sequences are each other's isoforms. The number of isoforms and paralogs in this allotetraploid species is of interest in the study of evolution. Conclusion We developed an SVM classifier that can be used to distinguish isoforms from paralogs with high accuracy and without access to the genomic data. It can be used to analyze, for example, EST data and database search results. Our software is freely available on the Web, under the name IsoSVM.
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Affiliation(s)
- Michael Spitzer
- Division of Bioinformatics, Biology Department, Schlossplatz 4, 48149 Münster, Germany
| | - Stefan Lorkowski
- Leibniz Institute of Arteriosclerosis Research, Domagkstr. 3, 48149 Münster, Germany
- Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Paul Cullen
- Leibniz Institute of Arteriosclerosis Research, Domagkstr. 3, 48149 Münster, Germany
| | - Alexander Sczyrba
- Faculty of Technology, Research Group in Practical Computer Science, University of Bielefeld,Postfach 10 01 31, 33501 Bielefeld, Germany
| | - Georg Fuellen
- Division of Bioinformatics, Biology Department, Schlossplatz 4, 48149 Münster, Germany
- Department of Medicine, AG Bioinformatics, Domagkstr. 3, 48149 Münster, Germany
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