Структура карточки блока OBJECT

 

ID: Идентификатор карточки блока OBJECT;

LOCATION: Расположение энхансера (5'UTR, 3’UTR, CDS);

TYPE: Тип энхансера (stress-specific и др.);

OC: Таксономическая классификация;

OS: Название вида;

GENE: Название гена;

CAP: Наличие кепа на 5’-конце мРНК;

POLYA Наличие поли(А)-участка на 3’-конце мРНК;

SQ: Собственно нуклеотидная последовательность энхансера;

COMMENTSEQ: Комментарий о расположении нуклеотидной последовательности энхансера в составе мРНК;

KEYWORD: Ключевые слова;

COMMENT: Комментарий о специфичности и активности энхансера;

LINK_ENH: Ссылка на идентификатор карточки блока ENHANCER;

LINK: Ссылка на банк данных нуклеотидных последовательностей;

END: Граница карточки.

 

Пример заполнения карточки в блоке OBJECT:

TGP_PROMOTER:Ps:TOP2_P3

ID ADHZM5

LOCATION 5'UTR

TYPE Stress-specific enhancer

OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; Zea

OS Zea mays

GENE ADH1, alcoholdehydrogenase I

CAP Capped

POLYA Polyadenylated

SQ ATTTTCTCGCTCCTCACAGGCTCATCTCGTTTGGATCGATTGGTTTCGTAACTGGTGAAGGA CTGAGGGTCTCGGAGTGGATCGATTTGGGATTCTGTTCGAAGATTTGCGGAGGGGGGCA

COMMENTSEQ 5'UTR of ADH1 gene mRNA

KEYWORD Enhancer, hypoxia, anoxia, anaerobiosis, stress

COMMENT It was found that translation of alcoholdehydrogenase mRNA was efficient under oxygen deprivation conditions whereas translation of many other mRNAs was stopped. No changes in mRNA stability were detected so the effect observed could result from the changes in stress-specific translation rate. Deletions of ADH 5'UTR decreased stress-specific translatability: the influence of possible changes in secondary structure was not tested or discussed. Interestingly, the presence of ADH 5'UTR did not affect translation under aerobic conditions.

LINK_ENH ADHZM5a

LINK EMBL_AC X00580

END

 

Структура карточки блока ENHANCER

 

ID Идентификатор карточки блока ENHANCER;

OBJID Ссылка на идентификатор карточки блока OBJECT;

SEQUENCE Нуклеотидная последовательность функционального района (5’-НТП, 3’-НТП), содержащего энхансер;

COMMENTSEQ Комментарий к структуре экспериментальной конструкции;

ORGANISM Видовое название организма, на котором проводили эксперименты;

KEYWORD Ключевые слова;

COMMENT Развернутый комментарий о специфичности и активности энхансера, эффективности его использования в различных видах организмов-рецепиентов;

REFERENCE Название статьи и ссылка на базу данных PubMed;

END Граница карточки.

 

Пример заполнения карточки в блоке ENHANCER

TGP_GENE:Ps:TOP2

 

ID ADHZM5a

SEQUENCE ATAGGGAGACCGAATTCGAGCTCATTTTCTCGCTCCTCACAGGCTCATCTCGTTTGGATCGATTGGTT TCGTAACTGGTGAAGGACTGAGGGTCTCGGAGTGGATCGATTTGGGATTCTGTTCGAAGATTTGCGGAGGGGGGCA

COMMENTSEQ Design of mRNA 5'UTR of GUS reporter gene: first 23 nt were taken from vector sequence followed by 108-nt long 5'UTR of ADH1. In this construct CDS consisted from 18 codons of ADH1 CDS fused to 8 codons derived from vector polylinker sequence and GUS CDS downstream. 3'UTR was represented by ADH mRNA 3'UTR.

ORGANISM Zea mays

KEYWORD Hypoxia, stress, 5’UTR, enhancer

COMMENT Translational efficiencies of reporter mRNAs containing UTR sequences of maize alcoholdehydrogenase gene mRNA were tested in maize protoplasts under normal or oxygen deprivation conditions. No changes in mRNA stability were detected so the effect observed resulted from the changes in stress-specific translation rate. Interestingly, the presence of ADH 5'UTR did not affect translation under aerobic conditions. Generally, deletions of ADH-derived fragments decreased stress-specific translatability: either deletion of first 18 ADH-derived codons or fragments of 5'UTR or 3'UTR. Note, that 5'portion of 5'UTR was presented in all constructions. The influence of possible changes in secondary structure was not tested or discussed. As was found ADH1 3'UTR mRNA increase hypoxia-specific translation 3.5-fold but decrease aerobic translation 3-fold.

REFERENCE Bailey-Serres J., Dawe R.K. Both 5' and 3' sequences of maize adh1 mRNA are required for enhanced translation under low-oxygen conditions. Plant Physiol. 1996. 112. 685-695 8883381

END