Protocol for Gene Expression Profiling Using DNA Microarrays in Neisseria gonorrhoeae

Jackson, Lydgia A.; Dyer, David W.

doi:10.1007/978-1-61779-937-2_24

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…The expression profiles can provide useful clues to gene functions ( Jackson and Dyer, 2012 ). Here, we used the expression levels of BrrOPT genes were reanalyzed using publicly available RNA sequence data from three different developmental stages ( Li et al., 2015 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Yang

Yin

et al. 2018

Plant Diversity

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Oligopeptide transporters (OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses revealed two well-supported clades in the OPT family, containing 15 BrrOPTs and 13 BrrYSLs. The exon/intron structure of OPT clade are conserved but the yellow stripe-like (YSL) clade was different. The exon/intron of the YSL clade possesses structural differences, whereas the YSL class motifs structure are conserved. The OPT genes are distributed unevenly among the chromosomes of the turnip genome. Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication. For the expression profiles at different developmental stages, a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family. Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution. Furthermore, BrrOPT8.1, BrrYSL1.2, BrrYSL1.3, BrrYSL6 and BrrYSL9 responded to Fe(II) treatments and BrrYSL7 responded to calcium treatments, BrrYSL6 responded to multiple treatments in root, suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies. Our data provide important information for further functional dissection of BrrOPTs, especially in transporting metal ions and nutrient deficiency stress adaptation.

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Section: Resultsmentioning

confidence: 99%

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Yang

Yin

et al. 2018

Plant Diversity

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“…This was done instead of using the Qiagen RNeasy columns to ensure that RNA of Ͻ200 bp was collected. Quantitation was done using the NanoDrop ND-100 spectrophotometer instrument (Thermo Scientific), and RNA integrity was assessed with an Agilent RNA 6000 Nano Kit on the Agilent 2100 bioanalyzer (28).…”

Section: Methodsmentioning

confidence: 99%

“…The QIAquick PCR purification kit (Qiagen) was used both to purify the cDNA after the removal of the RNA template and before labeling and to purify the biotinylated cDNA probes. A 3-g aliquot of biotin-labeled cDNA was hybridized to the custom 12K N. gonorrhoeae expression array, according to the CombiMatrix hybridization protocol (28). Arrays were hybridized at 50°C for 14 h before electrochemical detection using an ElectraSense reader (CombiMatrix).…”

Section: Methodsmentioning

confidence: 99%

Control of RNA Stability by NrrF, an Iron-Regulated Small RNA in Neisseria gonorrhoeae

et al. 2013

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bRegulation of gene expression by small noncoding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a trans-acting sRNA in Neisseria meningitidis and Neisseria gonorrhoeae, has been shown in the meningococcus to control indirectly, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms, sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including N. gonorrhoeae FA1090, an nrrF deletion mutant, and a complemented derivative, were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, the mRNA halflives for 12 genes under Fe-depleted growth conditions were longer than those in FA1090. The 12 genes controlled by NrrF encoded proteins with biological functions including energy metabolism, oxidative stress, antibiotic resistance, and amino acid synthesis, as well as hypothetical proteins and a regulatory protein whose functions are not fully understood.

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“…Expression profiles give useful information on gene functions [43]. Here, we reanalyzed the expression levels of callose GSL and endo-1,3-b-glucosidase genes using publicly available RNA sequence data of four different tissues [37].…”

Section: Callose Gsl and Endo-13-b-glucosidase Gene Expression Profil...mentioning

confidence: 99%

Genome‐wide analysis of the callose enzyme families of fertile and sterile flower buds of the Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Hou

Guo

et al. 2019

FEBS Open Bio

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Callose is a β‐1,3‐glucan commonly found in higher plants that plays an important role in regulating plant pollen development. It is synthesized by glucan synthase‐like (GSL) and is degraded by the enzyme endo‐1,3‐β‐glucosidase. However, genome‐wide analyses of callose GSL and endo‐1,3‐β‐glucosidase enzymes in fertile and sterile flower buds of Chinese cabbage have not yet been reported. Here, we show that delayed callose degradation at the tetrad stage may be the main cause of microspore abortion in Chinese cabbage with nuclear sterility near‐isogenic line ‘10L03’. Fifteen callose GSLs and 77 endo‐1,3‐β‐glucosidase enzymes were identified in Chinese cabbage. Phylogenetic, gene structural and chromosomal analyses revealed that the expansion occurred due to three polyploidization events of these two gene families. Expression pattern analysis showed that the GSL and endo‐1,3‐β‐glucosidase enzymes are involved in the development of various tissues and that the genes functionally diverged during long‐term evolution. Relative gene expression analysis of Chinese cabbage flowers at different developmental stages showed that high expression of the synthetic enzyme BraA01g041620 and low expression of AtA6‐homologous genes (BraA04g008040, BraA07g009320, BraA01g030220 and BraA03g040850) and two other genes (BraA10g020080 and BraA05g038340) for degrading enzymes in the meiosis and tetrad stages may cause nuclear sterility in the near‐isogenic line ‘10L03’. Overall, our data provide an important foundation for comprehending the potential roles of the callose GSL and endo‐1,3‐β‐glucosidase enzymes in regulating pollen development in Chinese cabbage.

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Protocol for Gene Expression Profiling Using DNA Microarrays in Neisseria gonorrhoeae

Cited by 6 publications

References 39 publications

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Control of RNA Stability by NrrF, an Iron-Regulated Small RNA in Neisseria gonorrhoeae

Genome‐wide analysis of the callose enzyme families of fertile and sterile flower buds of the Chinese cabbage (Brassica rapa L. ssp. pekinensis)

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