A new cysteine-rich protein-encoding gene family in Giardia duodenalis

This study investigated the effect of cefepime at sub-minimum inhibitory concentrations (sub-MICs) on in vitro biofilm formation (BF) by clinical isolates of Pseudomonas aeruginosa. The effect of cefepime at sub-MIC levels (½–1/256 MIC) on in vitro BF by six clinical isolates of P. aeruginosa was phenotypically assessed following 24 and 48 h of challenge using the tissue culture plate (TCP) assay. Quantitative real-time polymeric chain reaction (qRT-PCR) was employed to observe the change in expression of three biofilm-related genes, namely, a protease-encoding gene (lasA), fimbrial protein-encoding gene (cupA1), and alginate-encoding gene (algC), in a weak biofilm-producing strain of P. aeruginosa following 24 and 48 h of challenge with sub-MICs of cefepime. The BF morphology in response to cefepime was imaged using scanning electron microscopy (SEM). The TCP assay showed strain-, time-, and concentration-dependent changes in in vitro BF in P. aeruginosa following challenge with sub-MICs of cefepime, with a profound increase in strains with inherently no or weak biofilm-producing ability. RT-PCR revealed time-dependent upregulation in the expression of the investigated genes following challenge with ½ and ¼ MIC levels, as confirmed by SEM. Cefepime at sub-MICs could upregulate the expression of BF-related genes and enhance BF by P. aeruginosa clinical isolates.

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The Use of the Nuclear Protein-Encoding Gene, RNA Polymerase II, for Tick Molecular Systematics

Experimental and Applied Acarology ◽

10.1023/a:1025389914156 ◽

2002 ◽

Vol 28 (1-4) ◽

pp. 69-75 ◽

Cited By ~ 9

Author(s):

Quentin Fang ◽

James E. Keirans ◽

Tonya Mixson

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Molecular Systematics ◽

Nuclear Protein ◽

Protein Encoding ◽

Encoding Gene

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A Single Gene on the Staphylococcal Multiresistance Plasmid pSK1 Encodes a Novel Partitioning System

Journal of Bacteriology ◽

10.1128/jb.185.7.2143-2152.2003 ◽

2003 ◽

Vol 185 (7) ◽

pp. 2143-2152 ◽

Cited By ~ 40

Author(s):

Alice E. Simpson ◽

Ronald A. Skurray ◽

Neville Firth

Keyword(s):

Single Gene ◽

Replication Initiation ◽

Plasmid Replication ◽

Rolling Circle ◽

Plasmid Segregation ◽

Segregational Stability ◽

Protein Encoding ◽

Single Protein ◽

Encoding Gene ◽

Postsegregational Killing

ABSTRACT The orf245 gene is located immediately upstream of, and divergently transcribed from, the replication initiation gene, rep, of the Staphylococcus aureus multiresistance plasmid pSK1, and related genes have been found in association with a range of evolutionarily distinct replication genes on plasmids from various gram-positive genera. orf245 has been shown previously to extend the segregational stability of a pSK1 minireplicon. Here we describe an investigation into the basis of orf245-mediated stabilization. orf245 was not found to influence transcription of pSK1 rep, indicating that it is not directly involved in plasmid replication. This was confirmed by demonstrating that orf245 is able to enhance the segregational stability of heterologous theta- and rolling-circle-replicating replicons, suggesting that it encodes a plasmid maintenance function. Evidence inconsistent with postsegregational killing and multimer resolution mechanisms was obtained; however, the intergenic region upstream of orf245 was found to mediate orf245-dependent incompatibility, as would be expected if it encodes a cis-acting centromere-like site. Taken together, these findings implicate active partitioning as the probable basis of the activity of orf245, which is therefore redesignated par. Since it is unrelated to any gene known to play a role in plasmid segregation, it seems likely that pSK1 par potentially represents the prototype of a novel class of active partitioning systems that are distinguished by their capacity to enhance plasmid segregational stability via a single protein-encoding gene.

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Genome-wide analysis of chloride channel-encoding gene family members and identification of CLC genes that respond to Cl−/salt stress in upland cotton

Molecular Biology Reports ◽

10.1007/s11033-020-06023-z ◽

2020 ◽

Vol 47 (12) ◽

pp. 9361-9371

Author(s):

Xun Liu ◽

Boyi Pi ◽

Jianwei Pu ◽

Cong Cheng ◽

Jiajia Fang ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Chloride Channel ◽

Upland Cotton ◽

Family Members ◽

Genome Wide Analysis ◽

Genome Wide ◽

Encoding Gene

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Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer

PLoS ONE ◽

10.1371/journal.pone.0181596 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0181596 ◽

Cited By ~ 6

Author(s):

Rui Yin ◽

Mingzhu Zhao ◽

Kangyu Wang ◽

Yanping Lin ◽

Yanfang Wang ◽

...

Keyword(s):

Gene Family ◽

Panax Ginseng ◽

Functional Differentiation ◽

Encoding Gene

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Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears

BMC Genomics ◽

10.1186/s12864-020-07226-1 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Manyi Sun ◽

Mingyue Zhang ◽

Jugpreet Singh ◽

Bobo Song ◽

Zikai Tang ◽

...

Keyword(s):

Genetic Variation ◽

Disease Resistance ◽

Positive Selection ◽

Gene Family ◽

Selection Pressure ◽

Black Spot ◽

Orthologous Gene ◽

European Pear ◽

Encoding Gene ◽

Encoding Genes

Abstract Background The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’, an Asian pear) and Pyrus communis (‘Bartlett’, a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. Results In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. Conclusion Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.

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