Evolution and Expression of the Meprin and TRAF Homology Domain-Containing Gene Family in Solanaceae

Meprin and TRAF homology (MATH)-domain-containing proteins are pivotal in modulating plant development and environmental stress responses. To date, members of the MATH gene family have been identified only in a few plant species, including Arabidopsis thaliana, Brassica rapa, maize, and rice, and the functions of this gene family in other economically important crops, especially the Solanaceae family, remain unclear. The present study identified and analyzed 58 MATH genes from three Solanaceae species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum), and pepper (Capsicum annuum). Phylogenetic analysis and domain organization classified these MATH genes into four groups, consistent with those based on motif organization and gene structure. Synteny analysis found that segmental and tandem duplication might have contributed to MATH gene expansion in the tomato and the potato, respectively. Collinearity analysis revealed high conservation among Solanaceae MATH genes. Further cis-regulatory element prediction and gene expression analysis showed that Solanaceae MATH genes play essential roles during development and stress response. These findings provide a theoretical basis for other functional studies on Solanaceae MATH genes.

[1]  Wenqing Zhang,et al.  Poaceae-specific β-1,3;1,4-d-glucans link jasmonate signalling to OsLecRK1-mediated defence response during rice-brown planthopper interactions. , 2023, Plant biotechnology journal.

[2]  Yasuhito Sakuraba.  Molecular basis of nitrogen starvation-induced leaf senescence , 2022, Frontiers in Plant Science.

[3]  M. J. Skelly.  The emerging roles of deubiquitinases in plant proteostasis , 2022, Essays in biochemistry.

[4]  Juan Li,et al.  TRAF proteins as key regulators of plant development and stress responses. , 2021, Journal of integrative plant biology.

[5]  S. Xiao,et al.  Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum , 2020, Plants.

[6]  Peer Bork,et al.  SMART: recent updates, new developments and status in 2020 , 2020, Nucleic Acids Res..

[7]  J. Callis,et al.  The ubiquitin system affects agronomic plant traits , 2020, The Journal of Biological Chemistry.

[8]  S. Xiao,et al.  Evolution and Expression of the Membrane Attack Complex and Perforin Gene Family in the Poaceae , 2020, International journal of molecular sciences.

[9]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[10]  Takuya Norizuki,et al.  Role of Autophagy in Male Reproductive Processes in Land Plants , 2020, Frontiers in Plant Science.

[11]  A. Fernie,et al.  MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle. , 2020, Molecular plant.

[12]  D. Inzé,et al.  UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2 , 2020, eLife.

[13]  M. Chye,et al.  Polyunsaturated linolenoyl-CoA modulates ERF-VII-mediated hypoxia signaling in Arabidopsis. , 2020, Journal of integrative plant biology.

[14]  L. Voesenek,et al.  The role of ethylene in metabolic acclimations to low oxygen , 2019, The New phytologist.

[15]  Narmada Thanki,et al.  CDD/SPARCLE: the conserved domain database in 2020 , 2019, Nucleic Acids Res..

[16]  Chin-Mei Lee,et al.  GIGANTEA recruits the UBP12 and UBP13 deubiquitylases to regulate accumulation of the ZTL photoreceptor complex , 2019, Nature Communications.

[17]  N. Chua,et al.  Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. , 2019, The New phytologist.

[18]  Kyu-Young Whang,et al.  MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments , 2019, Nucleic Acids Res..

[19]  A. Abdul-Sater,et al.  The Evolving Role of TRAFs in Mediating Inflammatory Responses , 2019, Front. Immunol..

[20]  H. H. Park.  Structure of TRAF Family: Current Understanding of Receptor Recognition , 2018, Front. Immunol..

[21]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[22]  S. Farrona,et al.  Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones , 2018, Front. Plant Sci..

[23]  F. Liu,et al.  PepperHub, an Informatics Hub for the Chili Pepper Research Community. , 2017, Molecular plant.

[24]  N. Chua,et al.  The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses , 2017, Plant Cell.

[25]  Q. Wang,et al.  TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis[OPEN] , 2017, Plant Cell.

[26]  A. Pareek,et al.  MATH-Domain Family Shows Response toward Abiotic Stress in Arabidopsis and Rice , 2016, Front. Plant Sci..

[27]  Xin Li,et al.  Plant TRAF Proteins Regulate NLR Immune Receptor Turnover. , 2016, Cell host & microbe.

[28]  Michal Brylinski,et al.  Predicting protein interface residues using easily accessible on-line resources , 2015, Briefings Bioinform..

[29]  T. Dresselhaus,et al.  Phylogenetic analysis of the expansion of the MATH-BTB gene family in the grasses , 2014, Plant signaling & behavior.

[30]  A. Krogh,et al.  Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization , 2014, Proceedings of the National Academy of Sciences.

[31]  Yeisoo Yu,et al.  Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species , 2014, Nature Genetics.

[32]  Dan M. Bolser,et al.  Ensembl Genomes 2013: scaling up access to genome-wide data , 2013, Nucleic Acids Res..

[33]  A. Aharoni,et al.  Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes , 2013, Science.

[34]  Y. Ruan,et al.  Send Orders of Reprints at Reprints@benthamscience.net Phylogenetic Analysis of Brassica Rapa Math-domain Proteins , 2022 .

[35]  S. Eddy,et al.  Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.

[36]  S. Sprunck,et al.  Germline-Specific MATH-BTB Substrate Adaptor MAB1 Regulates Spindle Length and Nuclei Identity in Maize[W] , 2012, Plant Cell.

[37]  Alan Bridge,et al.  New and continuing developments at PROSITE , 2012, Nucleic Acids Res..

[38]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[39]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[40]  R. Ewan,et al.  Deubiquitinating enzymes AtUBP12 and AtUBP13 and their tobacco homologue NtUBP12 are negative regulators of plant immunity. , 2011, The New phytologist.

[41]  J. Carrington,et al.  RTM3, Which Controls Long-Distance Movement of Potyviruses, Is a Member of a New Plant Gene Family Encoding a Meprin and TRAF Homology Domain-Containing Protein1[W][OA] , 2010, Plant Physiology.

[42]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[43]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[44]  Kousuke Hanada,et al.  Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice[W] , 2007, The Plant Cell Online.

[45]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[46]  L. Schauser,et al.  Evolution of NIN-Like Proteins in Arabidopsis, Rice, and Lotus japonicus , 2005, Journal of Molecular Evolution.

[47]  M. Sunnerhagen,et al.  The new MATH: homology suggests shared binding surfaces in meprin tetramers and TRAF trimers , 2002, FEBS letters.

[48]  D. Vaux,et al.  TRAF proteins and meprins share a conserved domain. , 1996, Trends in biochemical sciences.

[49]  D. Goeddel,et al.  A novel family of putative signal transducers associated with the cytoplasmic domain of the 75 kDa tumor necrosis factor receptor , 1994, Cell.

[50]  T. Candresse,et al.  RTM3 which controls long distance movement of potyviruses is a member of a new plant gene family encoding a meprin and TRAF homology (MATH) domain-containing protein , 2010 .

[51]  S. Lefebvre,et al.  Phylogeny of the TRAF/MATH domain. , 2007, Advances in experimental medicine and biology.

[52]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..