A high‐efficient strategy for combinatorial engineering paralogous gene family: a case study on histidine kinases in Clostridium

2021 ◽  
Author(s):  
Chao Zhu ◽  
Guangqing Du ◽  
Jie Zhang ◽  
Chuang Xue
Keyword(s):  
Gene Family ◽  
Paralogous Gene ◽  
Histidine Kinases ◽  
Efficient Strategy ◽  
High Efficient ◽  
Combinatorial Engineering ◽  
Paralogous Gene Family

scholarly journals Temporal Expression Analysis of the Borrelia burgdorferi Paralogous Gene Family 54 Genes BBA64, BBA65, and BBA66 during Persistent Infection in Mice

2007 ◽  
Vol 75 (6) ◽  
pp. 2753-2764 ◽  
Author(s):  
Robert D. Gilmore ◽  
Rebekah R. Howison ◽  
Virginia L. Schmit ◽  
Andrew J. Nowalk ◽  
Dawn R. Clifton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Borrelia Burgdorferi ◽  
Gene Family ◽  
Expression Profile ◽  
Persistent Infection ◽  
Adaptive Immune Response ◽  
Paralogous Gene ◽  
Reverse Transcription Pcr ◽  
Paralogous Gene Family

ABSTRACT Members of the Borrelia burgdorferi paralogous gene family 54 (pgf 54) are regulated by conditions simulating mammalian infection and are thought to be instrumental in borrelial host survival and pathogenesis. To explore the activities of these genes in vivo, a comprehensive analysis of pgf 54 genes BBA64, BBA65, and BBA66 was performed to assess the genetic stability, host antibody responses, and kinetics of gene expression in the murine model of persistent infection. DNA sequencing of pgf 54 genes obtained from reisolates at 1 year postinfection demonstrated that all genes of this family are stable and do not undergo recombination to generate variant antigens during persistent infection. Antibodies against BBA64 and BBA66 appeared soon after infection and were detectable throughout the infection, suggesting that there was gene expression during infection. However, quantitative reverse transcription-PCR revealed that BBA64 gene expression was considerably decreased in Borrelia residing in the mouse ear tissue compared to the expression in cultured spirochetes by 20 days postinfection and that the levels of expression remained low throughout the infection. Conversely, transcription of the BBA65 and BBA66 genes was increased, and both of these genes were continuously expressed until 100 days postinfection; this was followed by periods of differential expression late in infection. The expression profile of the BBA64 gene suggests that this gene has an important role during tick-to-host transmission and early infection, whereas the expression profile of the BBA65 and BBA66 genes suggests that these genes have a role in persistent infection. The differential regulation of pgf 54 genes observed during infection may help confer a survival advantage during persistent infection, influencing mechanisms for B. burgdorferi dissemination, tissue tropism, or evasion of the adaptive immune response.

scholarly journals Identification of 11 pH-Regulated Genes inBorrelia burgdorferi Localizing to Linear Plasmids

2000 ◽  
Vol 68 (12) ◽  
pp. 6677-6684 ◽  
Author(s):  
James A. Carroll ◽  
Rebecca M. Cordova ◽  
Claude F. Garon
Keyword(s):  
Gene Family ◽  
Genomic Library ◽  
Ph Regulation ◽  
Protein Profile ◽  
Rabbit Serum ◽  
Mammalian Host ◽  
Paralogous Gene ◽  
Linear Plasmids ◽  
Paralogous Gene Family

ABSTRACT When Borrelia burgdorferi is transmitted from the tick vector to the mammalian host, the bacterium experiences alterations in its environment, such as changes in temperature and pH. Previously, we observed numerous alterations in the membrane protein profile whenB. burgdorferi B31 was grown at pH 7.0 compared to pH 8.0. Here we identify 11 genes localizing to linear plasmids that are up-regulated at pH 7.0 relative to pH 8.0 in vitro. Seven genes (bba03, bba24, bba64, bba66, bbe31, bbj41/bbi39 [encoding products that are 99% identical], and bbk01) were indirectly identified by proteomic analysis of membrane proteins. Another gene, bba36, was identified by screening a B. burgdorferi B31 genomic library with cross-adsorbed hyperimmune rabbit serum. Two additional genes, bba65 andbba73, were identified by Northern blot analysis. Genesbba64, bba65, bba66, bbj41/bbi39, and bba73 are members of paralogous gene family 54, and bbe31 is a member of the closely related paralogous gene family 60. Genebba24 is part of a bicistronic operon withbba25 that encodes the well-characterized decorin binding proteins A and B. All 11 genes were transcriptionally regulated, yet the degree of pH regulation varied, with some genes more tightly regulated than others. The regions upstream of these pH-regulated genes appeared to be unrelated, yet many contained dyad repeats ranging from 12 to 25 nucleotides in length that may be involved in the regulation of these genes.

High efficient strategy for the production of hydroxyapatite/silk sericin nanocomposites

2020 ◽  
Vol 96 (1) ◽  
pp. 241-248
Author(s):  
Anabela Veiga ◽  
Filipa Castro ◽  
Ana Oliveira ◽  
Fernando Rocha
Keyword(s):  
Silk Sericin ◽  
Efficient Strategy ◽  
High Efficient

scholarly journals Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

2020 ◽  
Vol 12 (3) ◽  
pp. 185-202
Author(s):  
Xia Han ◽  
Jindan Guo ◽  
Erli Pang ◽  
Hongtao Song ◽  
Kui Lin
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genome Phylogeny ◽  
Partial Homology

Abstract How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

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