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Sigalova OM, Chaplin AV, Bochkareva OO, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics 2019; 20:710. [PMID: 31510914 PMCID: PMC6740158 DOI: 10.1186/s12864-019-6059-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 01/23/2023] Open
Abstract
Background Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. Results We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system. Conclusions This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity. Electronic supplementary material The online version of this article (10.1186/s12864-019-6059-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olga M Sigalova
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,current address: European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrei V Chaplin
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga O Bochkareva
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia. .,current address: Institute of Science and Technology Austria, Klosterneuburg, Austria.
| | - Pavel V Shelyakin
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Vavilov Institute of General Genetics, RAS, Moscow, Russia
| | | | - Evgeny E Akkuratov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.,current address: Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Burskaia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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Ansari MY, Mande SC. A Glimpse Into the Structure and Function of Atypical Type I Chaperonins. Front Mol Biosci 2018; 5:31. [PMID: 29696145 PMCID: PMC5904260 DOI: 10.3389/fmolb.2018.00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
Chaperonins are a subclass of molecular chaperones that assist cellular proteins to fold and assemble into their native shape. Much work has been done on Type I chaperonins, which has elucidated their elegant mechanism. Some debate remains about the details in these mechanisms, but nonetheless the roles of these in helping protein folding have been understood in great depth. In this review we discuss the known functions of atypical Type I chaperonins, highlighting evolutionary aspects that might lead chaperonins to perform alternate functions.
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3
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Ke X, Zou W, Ren Y, Wang Z, Li J, Wu X, Zhao J. Functional divergence of chloroplast Cpn60α subunits during Arabidopsis embryo development. PLoS Genet 2017; 13:e1007036. [PMID: 28961247 PMCID: PMC5636168 DOI: 10.1371/journal.pgen.1007036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/11/2017] [Accepted: 09/20/2017] [Indexed: 02/03/2023] Open
Abstract
Chaperonins are a class of molecular chaperones that assist in the folding and assembly of a wide range of substrates. In plants, chloroplast chaperonins are composed of two different types of subunits, Cpn60α and Cpn60β, and duplication of Cpn60α and Cpn60β genes occurs in a high proportion of plants. However, the importance of multiple Cpn60α and Cpn60β genes in plants is poorly understood. In this study, we found that loss-of-function of CPNA2 (AtCpn60α2), a gene encoding the minor Cpn60α subunit in Arabidopsis thaliana, resulted in arrested embryo development at the globular stage, whereas the other AtCpn60α gene encoding the dominant Cpn60α subunit, CPNA1 (AtCpn60α1), mainly affected embryonic cotyledon development at the torpedo stage and thereafter. Further studies demonstrated that CPNA2 can form a functional chaperonin with CPNB2 (AtCpn60β2) and CPNB3 (AtCpn60β3), while the functional partners of CPNA1 are CPNB1 (AtCpn60β1) and CPNB2. We also revealed that the functional chaperonin containing CPNA2 could assist the folding of a specific substrate, KASI (β-ketoacyl-[acyl carrier protein] synthase I), and that the KASI protein level was remarkably reduced due to loss-of-function of CPNA2. Furthermore, the reduction in the KASI protein level was shown to be the possible cause for the arrest of cpna2 embryos. Our findings indicate that the two Cpn60α subunits in Arabidopsis play different roles during embryo development through forming distinct chaperonins with specific AtCpn60β to assist the folding of particular substrates, thus providing novel insights into functional divergence of Cpn60α subunits in plants. Chaperonins are large oligomeric complexes that are involved in the folding and assembly of numerous proteins in various species. In contrast to other types of chaperonins, chloroplast chaperonins are characterized by the hetero-oligomeric structure composed of two unique types of subunits, Cpn60α and Cpn60β, each of which is present in two or more paralogous forms in most of higher plants. However, the functional significance underlying the wide array of subunit types and complex oligomeric arrangement remains largely unknown. Here, we investigated the role of the minor Cpn60α subunit AtCpn60α2 in Arabidopsis embryo development, and found that AtCpn60α2 is important for the transition of globular embryos to heart-shaped embryos, whereas loss of the dominant Cpn60α subunit AtCpn60α1 affects embryonic cotyledon development. Further studies demonstrated that AtCpn60α2 could form functional chaperonins with AtCpn60β2 and AtCpn60β3 to specifically assist in folding of the substrate KASI, which is important for the formation of heart-shaped embryos. Our results suggest that duplication of Cpn60α genes in higher plants can increase the potential number of chloroplast chaperonin substrates and provide chloroplast chaperonins with more roles in plant growth and development, thus revealing the relationship between duplication and functional specialization of chaperonin genes.
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Affiliation(s)
- Xiaolong Ke
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafang Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhiqin Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jin Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xuan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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4
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Biochemical and Genetic Analysis of the Chlamydia GroEL Chaperonins. J Bacteriol 2017; 199:JB.00844-16. [PMID: 28396349 DOI: 10.1128/jb.00844-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/01/2017] [Indexed: 02/01/2023] Open
Abstract
Chaperonins are essential for cellular growth under normal and stressful conditions and consequently represent one of the most conserved and ancient protein classes. The paradigm Escherichia coli chaperonin, EcGroEL, and its cochaperonin, EcGroES, assist in the folding of proteins via an ATP-dependent mechanism. In addition to the presence of groEL and groES homologs, groEL paralogs are found in many bacteria, including pathogens, and have evolved poorly understood species-specific functions. Chlamydia spp., which are obligate intracellular bacteria, have reduced genomes that nonetheless contain three groEL genes, Chlamydia groEL (ChgroEL), ChgroEL2, and ChgroEL3 We hypothesized that ChGroEL is the bona fide chaperonin and that the paralogs perform novel Chlamydia-specific functions. To test our hypothesis, we investigated the biochemical properties of ChGroEL and its cochaperonin, ChGroES, and queried the in vivo essentiality of the three ChgroEL genes through targeted mutagenesis in Chlamydia trachomatis ChGroEL hydrolyzed ATP at a rate 25% of that of EcGroEL and bound with high affinity to ChGroES, and the ChGroEL-ChGroES complex could refold malate dehydrogenase (MDH). The chlamydial ChGroEL was selective for its cognate cochaperonin, ChGroES, while EcGroEL could function with both EcGroES and ChGroES. A P35T ChGroES mutant (ChGroESP35T) reduced ChGroEL-ChGroES interactions and MDH folding activities but was tolerated by EcGroEL. Both ChGroEL-ChGroES and EcGroEL-ChGroESP35T could complement an EcGroEL-EcGroES mutant. Finally, we successfully inactivated both paralogs but not ChgroEL, leading to minor growth defects in cell culture that were not exacerbated by heat stress. Collectively, our results support novel functions for the paralogs and solidify ChGroEL as a bona fide chaperonin that is biochemically distinct from EcGroEL.IMPORTANCEChlamydia is an important cause of human diseases, including pneumonia, sexually transmitted infections, and trachoma. The chlamydial chaperonin ChGroEL and chaperonin paralog ChGroEL2 have been associated with survival under stress conditions, and ChGroEL is linked with immunopathology elicited by chlamydial infections. However, their exact roles in bacterial survival and disease remain unclear. Our results further substantiate the hypotheses that ChGroEL is the primary chlamydial chaperonin and that the paralogs play specialized roles during infection. Furthermore, ChGroEL and the mitochondrial GroEL only functioned with their cochaperonin, in contrast to the promiscuous nature of GroEL from E. coli and Helicobacter pylori, which might indicate a divergent evolution of GroEL during the transition from a free-living organism to an obligate intracellular lifestyle.
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5
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Fares MA. Evolution of Multiple Chaperonins: Innovation of Evolutionary Capacitors. PROKARYOTIC CHAPERONINS 2017:149-170. [DOI: 10.1007/978-981-10-4651-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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6
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Astaxanthin biosynthetic pathway: Molecular phylogenies and evolutionary behaviour of Crt genes in eubacteria. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Garzón-Ospina D, Forero-Rodríguez J, Patarroyo MA. Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis. BMC Evol Biol 2016; 16:256. [PMID: 27894257 PMCID: PMC5126858 DOI: 10.1186/s12862-016-0830-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The merozoite surface protein 7 (MSP7) is a Plasmodium protein which is involved in parasite invasion; the gene encoding it belongs to a multigene family. It has been proposed that MSP7 paralogues seem to be functionally redundant; however, recent experiments have suggested that they could have different roles. Results The msp7 multigene family has been described in newly available Plasmodium genomes; phylogenetic relationships were established in 12 species by using different molecular evolutionary approaches for assessing functional divergence amongst MSP7 members. Gene expansion and contraction rule msp7 family evolution; however, some members could have had concerted evolution. Molecular evolutionary analysis showed that relaxed and/or intensified selection modulated Plasmodium msp7 paralogous evolution. Furthermore, episodic diversifying selection and changes in evolutionary rates suggested that some paralogous proteins have diverged functionally. Conclusions Even though msp7 has mainly evolved in line with a birth-and-death evolutionary model, gene conversion has taken place between some paralogous genes allowing them to maintain their functional redundancy. On the other hand, the evolutionary rate of some MSP7 paralogs has become altered, as well as undergoing relaxed or intensified (positive) selection, suggesting functional divergence. This could mean that some MSP7s can form different parasite protein complexes and/or recognise different host receptors during parasite invasion. These results highlight the importance of this gene family in the Plasmodium genus. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0830-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego Garzón-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia.,PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, DC, Colombia
| | - Johanna Forero-Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50#26-20, Bogotá, DC, Colombia. .,School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24#63C-69, Bogotá, DC, Colombia.
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8
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Fares MA. Coevolution Analysis Illuminates the Evolutionary Plasticity of the Chaperonin System GroES/L. STRESS AND ENVIRONMENTAL REGULATION OF GENE EXPRESSION AND ADAPTATION IN BACTERIA 2016:796-811. [DOI: 10.1002/9781119004813.ch77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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9
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Funahashi A, Hiroi N. Simulation technology and its application in Systems Biology. Nihon Yakurigaku Zasshi 2016; 147:101-6. [PMID: 26860650 DOI: 10.1254/fpj.147.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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The evolution of protein moonlighting: adaptive traps and promiscuity in the chaperonins. Biochem Soc Trans 2015; 42:1709-14. [PMID: 25399594 DOI: 10.1042/bst20140225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Moonlighting proteins exhibit functions that are alternative to their main role in the cell. Heat-shock proteins, also known as molecular chaperones, are now recognized for their wide range of activities in and/or outside the cell, being prominent examples of moonlighting proteins. Chaperonins are highly conserved molecular chaperones that fold other proteins into their native conformation allowing them to carry out essential functions in the cell. Activities alternative to folding have been reported for the chaperonin (Cpn) 60 protein. Preservation of various alternative functions in one protein conflicts with the optimization of each of the functions. What evolutionary mechanisms have allowed the persistence of moonlighting proteins, and in particular the chaperonins, remains a mystery. In the present article, I argue that mechanisms that increase the resistance of phenotypes to genetic and environmental perturbations enable the persistence of a reservoir of genetic variants, each potentially codifying for a distinct function. Gene duplication is one such mechanism that has characterized the expansion and has been concomitant with the emergence of novel functions in these protein families. Indeed, Cpn60 performs a large list of folding-independent functions, including roles in the transmission of viruses from insects to plants and stimulation of the immune system, among others. In addition to the innovation promoted by gene duplication, I discuss that the Cpn60 protein comprises a hidden amino acid combinatorial code that may well be responsible for its ability to develop novel functions while maintaining an optimized folding ability. The present review points to a complex model of evolution of protein moonlighting.
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11
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Hanson BR, Tan M. Transcriptional regulation of the Chlamydia heat shock stress response in an intracellular infection. Mol Microbiol 2015; 97:1158-67. [PMID: 26075961 DOI: 10.1111/mmi.13093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2015] [Indexed: 11/30/2022]
Abstract
Bacteria encode heat shock proteins that aid in survival during stressful growth conditions. In addition, the major heat shock proteins of the intracellular bacterium Chlamydia trachomatis have been associated with immune pathology and disease. We developed a ChIP-qPCR method to study the regulation of chlamydial heat shock gene regulation during an intracellular infection. This approach allowed us to show that chlamydial heat shock genes are regulated by the transcription factor HrcA within an infected cell, providing validation for previous in vitro findings. Induction of chlamydial heat shock gene expression by elevated temperature was due to loss of HrcA binding to heat shock promoters, supporting a mechanism of derepression. This heat shock response was rapid, whereas recovery of HrcA binding and return to non-stress transcript levels occurred more slowly. We also found that control of heat shock gene expression was differentially regulated over the course of the intracellular Chlamydia infection. There was evidence of HrcA-mediated regulation of heat shock genes throughout the chlamydial developmental cycle, but the level of repression was lower at early times. This is the first study of Chlamydia-infected cells showing the effect of an environmental signal on transcription factor-DNA binding and target gene expression in the bacterium.
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Affiliation(s)
- Brett R Hanson
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Ming Tan
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA.,Department of Medicine, University of California, Irvine, CA, USA
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12
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Chowdhury N, Kingston JJ, Whitaker WB, Carpenter MR, Cohen A, Boyd EF. Sequence and expression divergence of an ancient duplication of the chaperonin groESEL operon in Vibrio species. MICROBIOLOGY-SGM 2014; 160:1953-1963. [PMID: 24913685 DOI: 10.1099/mic.0.079194-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Heat-shock proteins are molecular chaperones essential for protein folding, degradation and trafficking. The human pathogen Vibrio vulnificus encodes a copy of the groESEL operon in both chromosomes and these genes share <80 % similarity with each other. Comparative genomic analysis was used to determine whether this duplication is prevalent among Vibrionaceae specifically or Gammaproteobacteria in general. Among the Vibrionaceae complete genome sequences in the database (31 species), seven Vibrio species contained a copy of groESEL in each chromosome, including the human pathogens Vibrio cholerae, Vibrio parahaemolyticus and V. vulnificus. Phylogenetic analysis of GroEL among the Gammaproteobacteria indicated that GroESEL-1 encoded in chromosome I was the ancestral copy and GroESEL-2 in chromosome II arose by an ancient gene duplication event. Interestingly, outside of the Vibrionaceae within the Gammaproteobacteria, groESEL chromosomal duplications were rare among the 296 genomes examined; only five additional species contained two or more copies. Examination of the expression pattern of groEL from V. vulnificus cells grown under different conditions revealed differential expression between the copies. The data demonstrate that groEL-1 was more highly expressed during growth in exponential phase than groEL-2 and a similar pattern was also found in both V. cholerae and V. parahaemolyticus. Overall these data suggest that retention of both copies of groESEL in Vibrio species may confer an evolutionary advantage.
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Affiliation(s)
- Nityananda Chowdhury
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Joseph J Kingston
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - W Brian Whitaker
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Megan R Carpenter
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Analuisa Cohen
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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13
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Ruiz-González MX, Fares MA. Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L. BMC Evol Biol 2013; 13:156. [PMID: 23875653 PMCID: PMC3728108 DOI: 10.1186/1471-2148-13-156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GroESL is a heat-shock protein ubiquitous in bacteria and eukaryotic organelles. This evolutionarily conserved protein is involved in the folding of a wide variety of other proteins in the cytosol, being essential to the cell. The folding activity proceeds through strong conformational changes mediated by the co-chaperonin GroES and ATP. Functions alternative to folding have been previously described for GroEL in different bacterial groups, supporting enormous functional and structural plasticity for this molecule and the existence of a hidden combinatorial code in the protein sequence enabling such functions. Describing this plasticity can shed light on the functional diversity of GroEL. We hypothesize that different overlapping sets of amino acids coevolve within GroEL, GroES and between both these proteins. Shifts in these coevolutionary relationships may inevitably lead to evolution of alternative functions. RESULTS We conducted the first coevolution analyses in an extensive bacterial phylogeny, revealing complex networks of evolutionary dependencies between residues in GroESL. These networks differed among bacterial groups and involved amino acid sites with functional importance and others with previously unsuspected functional potential. Coevolutionary networks formed statistically independent units among bacterial groups and map to structurally continuous regions in the protein, suggesting their functional link. Sites involved in coevolution fell within narrow structural regions, supporting dynamic combinatorial functional links involving similar protein domains. Moreover, coevolving sites within a bacterial group mapped to regions previously identified as involved in folding-unrelated functions, and thus, coevolution may mediate alternative functions. CONCLUSIONS Our results highlight the evolutionary plasticity of GroEL across the entire bacterial phylogeny. Evidence on the functional importance of coevolving sites illuminates the as yet unappreciated functional diversity of proteins.
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Affiliation(s)
- Mario X Ruiz-González
- Integrative and Systems Biology Group, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC-UPV), Valencia, SPAIN
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Henderson B, Fares MA, Lund PA. Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biol Rev Camb Philos Soc 2013; 88:955-87. [DOI: 10.1111/brv.12037] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 02/20/2013] [Accepted: 03/04/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Brian Henderson
- Department of Microbial Diseases, UCL-Eastman Dental Institute; University College London; London WC1X 8LD U.K
| | - Mario A. Fares
- Department of Genetics; University of Dublin, Trinity College Dublin; Dublin 2 Ireland
- Department of Abiotic Stress; Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas (CSIC-UPV); Valencia 46022 Spain
| | - Peter A. Lund
- School of Biosciences; University of Birmingham; Birmingham B15 2TT U.K
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15
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The ecology of bacterial genes and the survival of the new. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:394026. [PMID: 22900231 PMCID: PMC3415099 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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16
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Abstract
Host-adapted bacteria include mutualists and pathogens of animals, plants and insects. Their study is therefore important for biotechnology, biodiversity and human health. The recent rapid expansion in bacterial genome data has provided insights into the adaptive, diversifying and reductive evolutionary processes that occur during host adaptation. The results have challenged many pre-existing concepts built from studies of laboratory bacterial strains. Furthermore, recent studies have revealed genetic changes associated with transitions from parasitism to mutualism and opened new research avenues to understand the functional reshaping of bacteria as they adapt to growth in the cytoplasm of a eukaryotic host.
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17
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Abstract
The evolution of protein function appears to involve alternating periods of conservative evolution and of relatively rapid change. Evidence for such episodic evolution, consistent with some theoretical expectations, comes from the application of increasingly sophisticated models of evolution to large sequence datasets. We present here some of the recent methods to detect functional shifts, using amino acid or codon models. Both provide evidence for punctual shifts in patterns of amino acid conservation, including the fixation of key changes by positive selection. Although a link to gene duplication, a presumed source of functional changes, has been difficult to establish, this episodic model appears to apply to a wide variety of proteins and organisms.
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Abstract
In addition to the nuclear genome, organisms have organelle genomes. Most of the DNA present in eukaryotic organisms is located in the cell nucleus. Chloroplasts have independent genomes which are inherited from the mother. Duplicated genes are common in the genomes of all organisms. It is believed that gene duplication is the most important step for the origin of genetic variation, leading to the creation of new genes and new gene functions. Despite the fact that extensive gene duplications are rare among the chloroplast genome, gene duplication in the chloroplast genome is an essential source of new genetic functions and a mechanism of neo-evolution. The events of gene transfer between the chloroplast genome and nuclear genome via duplication and subsequent recombination are important processes in evolution. The duplicated gene or genome in the nucleus has been the subject of several recent reviews. In this review, we will briefly summarize gene duplication and evolution in the chloroplast genome. Also, we will provide an overview of gene transfer events between chloroplast and nuclear genomes.
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19
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Abstract
A significant proportion of bacteria express two or more chaperonin genes. Chaperonins are a group of molecular chaperones, defined by sequence similarity, required for the folding of some cellular proteins. Chaperonin monomers have a mass of c. 60 kDa, and are typically found as large protein complexes containing 14 subunits arranged in two rings. The mechanism of action of the Escherichia coli GroEL protein has been studied in great detail. It acts by binding to unfolded proteins and enabling them to fold in a protected environment where they do not interact with any other proteins. GroEL can assist the folding of many proteins of different sizes, sequences, and structures, and homologues from many different bacteria can functionally replace GroEL in E. coli. What then are the functions of multiple chaperonins? Do they provide a mechanism for cells to increase their general chaperoning ability, or have they become specialized to take on specific novel cellular roles? Here I will review the genetic, biochemical, and phylogenetic evidence that has a bearing on this question, and show that there is good evidence for at least some specificity of function in multiple chaperonin genes.
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Affiliation(s)
- Peter A Lund
- School of Biosciences, University of Birmingham, Birmingham, UK.
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20
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Weiss C, Bonshtien A, Farchi-Pisanty O, Vitlin A, Azem A. Cpn20: siamese twins of the chaperonin world. PLANT MOLECULAR BIOLOGY 2009; 69:227-38. [PMID: 19031045 DOI: 10.1007/s11103-008-9432-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 11/08/2008] [Indexed: 05/08/2023]
Abstract
The chloroplast cpn20 protein is a functional homolog of the cpn10 co-chaperonin, but its gene consists of two cpn10-like units joined head-to-tail by a short chain of amino acids. This double protein is unique to plastids and was shown to exist in plants as well plastid-containing parasites. In vitro assays showed that this cpn20 co-chaperonin is a functional homolog of cpn10. In terms of structure, existing data indicate that the oligomer is tetrameric, yet it interacts with a heptameric cpn60 partner. Thus, the functional oligomeric structure remains a mystery. In this review, we summarize what is known about this distinctive chaperonin and use a bioinformatics approach to examine the expression of cpn20 in Arabidopsis thaliana relative to other chaperonin genes in this species. In addition, we examine the primary structure of the two homologous domains for similarities and differences, in comparison with cpn10 from other species. Lastly, we hypothesize as to the oligomeric structure and raison d'être of this unusual co-chaperonin homolog.
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Affiliation(s)
- Celeste Weiss
- Department of Biochemistry, Tel Aviv University, Tel Aviv, Israel
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21
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Leclerque A, Kleespies RG. 16S rRNA-, GroEL- and MucZ-based assessment of the taxonomic position of 'Rickettsiella melolonthae' and its implications for the organization of the genus Rickettsiella. Int J Syst Evol Microbiol 2008; 58:749-55. [PMID: 18398164 DOI: 10.1099/ijs.0.65359-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
'Rickettsiella melolonthae' is an intracellularly multiplying bacterial pathogen of European cockchafers, Melolontha melolontha (Linnaeus, 1758) and Melolontha hippocastani (Fabricius, 1801) (Coleoptera: Scarabaeidae). We report the first determination of nucleotide sequences from this organism, i.e. the 16S rRNA encoding rrs gene, the chaperonin encoding groEL gene and the mucZ gene encoding the orthologue of a capsule synthesis-inducing factor of Coxiella burnetii. Within the genus Rickettsiella, the pathotype 'Rickettsiella melolonthae' is currently classified as a synonym of the nomenclatural type species Rickettsiella popilliae. Previous sequencing of a 16S rRNA gene from a different species, Rickettsiella grylli, has motivated the transfer of the entire genus from the alphaproteobacterial order Rickettsiales to the gammaproteobacterial order Legionellales, family Coxiellaceae. We investigated the validity of this taxonomic reorganization beyond the species Rickettsiella grylli by reconstructing the organismal phylogeny from comparisons of 16S rRNA gene and GroEL and MucZ protein sequences from a selected set of alpha- and gammaproteobacteria as well as bacterial pathogens from the order Chlamydiales. Our analysis strongly supported the transfer of the genus Rickettsiella to the order Legionellales, but not its classification in one of the recognized families present in this order. Furthermore, our results substantiated inconsistencies in the internal organization of the genus. In particular, the currently accepted delineation of Rickettsiella species and the claimed synonymy of 'Rickettsiella melolonthae' with Rickettsiella popilliae are not simultaneously consistent with our findings.
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Affiliation(s)
- Andreas Leclerque
- Federal Biological Research Centre for Agriculture and Forestry (BBA), Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany.
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22
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Zaretsky JZ, Wreschner DH. Protein multifunctionality: principles and mechanisms. TRANSLATIONAL ONCOGENOMICS 2008; 3:99-136. [PMID: 21566747 PMCID: PMC3022353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the review, the nature of protein multifunctionality is analyzed. In the first part of the review the principles of structural/functional organization of protein are discussed. In the second part, the main mechanisms involved in development of multiple functions on a single gene product(s) are analyzed. The last part represents a number of examples showing that multifunctionality is a basic feature of biologically active proteins.
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Affiliation(s)
- Joseph Z Zaretsky
- Department Cell Research and Immunology, George Wise Faculty of Life Sciences, Tel-Aviv University, Ramat-Aviv, Haim Levanon St., 69978 Tel-Aviv, Israel
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23
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Kassai-Jáger E, Ortutay C, Tóth G, Vellai T, Gáspári Z. Distribution and evolution of short tandem repeats in closely related bacterial genomes. Gene 2007; 410:18-25. [PMID: 18191346 DOI: 10.1016/j.gene.2007.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 11/08/2007] [Accepted: 11/16/2007] [Indexed: 11/27/2022]
Abstract
Simultaneous identification and comparison of perfect and imperfect microsatellites within a genome is a valuable tool both to overcome the lack of a consensus definition of SSRs and to assess repeat history. Detailed analysis of the overall distribution of perfect and imperfect microsatellites in closely related bacterial taxa is expected to give new insight into the evolution of prokaryotic genomes. We have performed a genome-wide analysis of microsatellite distribution in four Escherichia coli and seven Chlamydial strains. Chlamydial strains generally have a higher density of SSRs and show greater intra-group differences of SSR distribution patterns than E. coli genomes. In most investigated genomes the distribution of the total lengths of matching perfect and imperfect trinucleotide repeats are highly similar, with the notable exception of C. muridarum. Closely related strains show more similar repeat distribution patterns than strains separated by a longer divergence time. The discrepancy between the preferred classes of perfect and imperfect repeats in C. muridarum implies accelerated evolution of SSRs in this particular strain. Our results suggest that microsatellites, although considerably less abundant than in eukaryotic genomes, may nevertheless play an important role in the evolution of prokaryotic genomes and several gene families.
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Affiliation(s)
- Edit Kassai-Jáger
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
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